Heck, I see it all the time in the forums. I've been called by large fortune 500 companies with SEO issues. I've seen more than once, they have a noindex tag on their home page causing the issue. Sometimes they are hard to spot due to redirects, so use a http header checker tool to verify before the redirects.

But don't overlook the obvious, check that first.

John Mueller of Google spotted a complaint in the Google Webmaster Help forums and after a day of back and forth between the site owner and people in the forum, John came in and said - it is more obvious than that.

It looks like a lot of your pages had a noindex robots meta tag on them for a while and dropped out because of that. In the meantime, that meta tag is gone, so if you can keep it out, you should be good to go :).

Of course, Google knows that because they have those details but if you hide those details from SEOs and remove the meta tag before they see the issue - then what.